Journal: Briefings in Bioinformatics

Volume 24, Issue 5

0 -- 0Yan Li, Shao-Wu Zhang, Ming-Yu Xie, Tong Zhang. PhenoDriver: interpretable framework for studying personalized phenotype-associated driver genes in breast cancer
0 -- 0Zhongying Ru, Yangyang Wu, Jinning Shao, Jianwei Yin, Linghui Qian, Xiaoye Miao. A dual-modal graph learning framework for identifying interaction events among chemical and biotech drugs
0 -- 0S. M. Bargeen Alam Turzo, Justin T. Seffernick, Sergey Lyskov, Steffen Lindert. Predicting ion mobility collision cross sections using projection approximation with ROSIE-PARCS webserver
0 -- 0Tingting Zhao, Lihua Cao, Jiafu Ji, David K. Chang, Jianmin Wu. ReProMSig: an integrative platform for development and application of reproducible multivariable models for cancer prognosis supporting guideline-based transparent reporting
0 -- 0Shengming Zhou, Yetong Zhou, Tian Liu, Jia Zheng, Cangzhi Jia. PredLLPS_PSSM: a novel predictor for liquid-liquid protein separation identification based on evolutionary information and a deep neural network
0 -- 0Chengming Zhang 0003, Yiwen Yang, Shijie Tang, Kazuyuki Aihara, Chuanchao Zhang, Luonan Chen. Contrastively generative self-expression model for single-cell and spatial multimodal data
0 -- 0Hunyong Cho, Yixiang Qu, Chuwen Liu, Boyang Tang, Ruiqi Lyu, Bridget M. Lin, Jeffrey Roach, M. Andrea Azcarate-Peril, Apoena Aguiar Ribeiro, Michael I. Love, Kimon Divaris, Di Wu. Comprehensive evaluation of methods for differential expression analysis of metatranscriptomics data
0 -- 0Jianfeng Sun, Arulsamy Kulandaisamy, Jinlong Ru, M. Michael Gromiha, Adam P. Cribbs. TMKit: a Python interface for computational analysis of transmembrane proteins
0 -- 0Lindsay Lee, Miao Yu, Xiaoqi Li, Chenxu Zhu, Yanxiao Zhang, Hongyu Yu, Ziyin Chen, Shreya Mishra, Bing Ren, Yun Li, Ming Hu 0001. SnapHiC-D: a computational pipeline to identify differential chromatin contacts from single-cell Hi-C data
0 -- 0Jiayi Liu, Anat Kreimer, Wei Vivian Li. Differential variability analysis of single-cell gene expression data
0 -- 0Nan Sheng, Yan Wang 0028, Lan Huang 0002, Ling Gao, Yangkun Cao, Xuping Xie, Yuan Fu. Multi-task prediction-based graph contrastive learning for inferring the relationship among lncRNAs, miRNAs and diseases
0 -- 0Mona Nourbakhsh, Astrid Saksager, Nikola Tom, Xi Steven Chen, Antonio Colaprico, Catharina Olsen, Matteo Tiberti, Elena Papaleo. A workflow to study mechanistic indicators for driver gene prediction with Moonlight
0 -- 0Tao Cui, Tingting Wang. A comprehensive assessment of hurdle and zero-inflated models for single cell RNA-sequencing analysis
0 -- 0David Martínez-Enguita, Sanjiv K. Dwivedi, Rebecka Jörnsten, Mika Gustafsson. NCAE: data-driven representations using a deep network-coherent DNA methylation autoencoder identify robust disease and risk factor signatures
0 -- 0Ko Abe, Teppei Shimamura. UNMF: a unified nonnegative matrix factorization for multi-dimensional omics data
0 -- 0Shudong Wang, Chuanru Ren, Yulin Zhang, YunYin Li, Shanchen Pang, Tao Song 0001. γ-norm regularization
0 -- 0Juan D. Henao, Michael Lauber, Manuel Azevedo, Anastasiia Grekova, Fabian Theis, Markus List, Christoph Ogris, Benjamin Schubert. Multi-omics regulatory network inference in the presence of missing data
0 -- 0Tianjiao Zhang, Liangyu Li, Hailong Sun, Dali Xu, Guohua Wang. DeepICSH: a complex deep learning framework for identifying cell-specific silencers and their strength from the human genome
0 -- 0Runzhou Yu, Syed Muhammad Umer Abdullah, Yanni Sun. HMMPolish: a coding region polishing tool for TGS-sequenced RNA viruses
0 -- 0Jiali Pang, Bilin Liang, Ruifeng Ding, Qiujuan Yan, Ruiyao Chen, Jie Xu. A denoised multi-omics integration framework for cancer subtype classification and survival prediction
0 -- 0Jingjing Wang, Werner Pieter Veldsman, Xiaodong Fang, Yufen Huang, Xuefeng Xie, Aiping Lyu, Lu Zhang 0061. Benchmarking multi-platform sequencing technologies for human genome assembly
0 -- 0Jian Gao, Zheyuan Shen, Yufeng Xie, Jialiang Lu, Yang Lu, Sikang Chen, Qingyu Bian, Yue Guo, Liteng Shen, Jian Wu, Binbin Zhou, Tingjun Hou, Qiaojun He, Jinxin Che, Xiaowu Dong. TransFoxMol: predicting molecular property with focused attention
0 -- 0Lejin Tian, Yunxiao Xie, Zhaobin Xie, Jasmine Tian, Weidong Tian. AtacAnnoR: a reference-based annotation tool for single cell ATAC-seq data
0 -- 0Jun Wang, Marc Horlacher, Lixin Cheng, Ole Winther. RNA trafficking and subcellular localization - a review of mechanisms, experimental and predictive methodologies
0 -- 0Robert Wang, Ingo Helbig, Andrew C. Edmondson, Lan Lin, Yi Xing. Splicing defects in rare diseases: transcriptomics and machine learning strategies towards genetic diagnosis
0 -- 0Na Lu, Yi Qiao, Pengfei An, Jiajian Luo, Changwei Bi, Musheng Li, Zuhong Lu, Jing Tu. Exploration of whole genome amplification generated chimeric sequences in long-read sequencing data
0 -- 0Hendrick Gao-Min Lim, Yang C. Fann, Yuan-Chii Gladys Lee. COWID: an efficient cloud-based genomics workflow for scalable identification of SARS-COV-2
0 -- 0Hongyan Gao, Jianqiang Sun, Yukun Wang, Yuer Lu, Liyu Liu, Qi Zhao, Jianwei Shuai. Predicting metabolite-disease associations based on auto-encoder and non-negative matrix factorization
0 -- 0Yuansheng Liu, Xiangzhen Shen, Yongshun Gong, Yiping Liu, Bosheng Song, Xiangxiang Zeng. Sequence Alignment/Map format: a comprehensive review of approaches and applications
0 -- 0Baiqing Li, Ting Ran, Hongming Chen. 3D based generative PROTAC linker design with reinforcement learning
0 -- 0Qingyong Wang, Minfan He, Long-Yi Guo, Hua Chai. AFEI: adaptive optimized vertical federated learning for heterogeneous multi-omics data integration
0 -- 0Kai Chen, Xiaodong Zhu 0001, Jiahao Wang, Ziqi Zhao, Lei Hao, Xinsheng Guo, Yuanning Liu. MFPred: prediction of ncRNA families based on multi-feature fusion
0 -- 0He Wang, Yongjian Zang, Ying Kang, Jianwen Zhang, Lei Zhang 0180, Shengli Zhang. ETLD: an encoder-transformation layer-decoder architecture for protein contact and mutation effects prediction
0 -- 0Quentin Blampey, Nadège Bercovici, Charles-Antoine Dutertre, Isabelle Pic, Joana Mourato Ribeiro, Fabrice André, Paul-Henry Cournède. A biology-driven deep generative model for cell-type annotation in cytometry
0 -- 0Shangru Jia, Artem Lysenko, Keith A. Boroevich, Alok Sharma, Tatsuhiko Tsunoda. scDeepInsight: a supervised cell-type identification method for scRNA-seq data with deep learning
0 -- 0Tong Liu, Zheng Wang. HiC4D: forecasting spatiotemporal Hi-C data with residual ConvLSTM
0 -- 0Xiaobo Yang, Bei Zhang, Siqi Wang, Ye Lu, Kaixian Chen, Cheng Luo, Aihua Sun, Hao Zhang. OTTM: an automated classification tool for translational drug discovery from omics data
0 -- 0Jun Wu, Haipeng Qing, Jian Ouyang, Jiajia Zhou, Zihao Gao, Christopher E. Mason, Zhichao Liu, Tieliu Shi. HiFun: homology independent protein function prediction by a novel protein-language self-attention model
0 -- 0Pora Kim, Himansu Kumar, Chengyuan Yang, Ruihan Luo, Jiajia Liu, Xiaobo Zhou. Systematic investigation of the homology sequences around the human fusion gene breakpoints in pan-cancer - bioinformatics study for a potential link to MMEJ
0 -- 0Shudong Wang, YunYin Li, Yuanyuan Zhang, Shanchen Pang, Sibo Qiao, Yu Zhang, Fuyu Wang. Generative Adversarial Matrix Completion Network based on Multi-Source Data Fusion for miRNA-Disease Associations Prediction
0 -- 0Yuchi Qiu, Guo-Wei Wei. Artificial intelligence-aided protein engineering: from topological data analysis to deep protein language models
0 -- 0Bo Wang, Jiawei Luo 0001, Ying Liu, Wanwan Shi, Zehao Xiong, Cong Shen 0002, Yahui Long. Spatial-MGCN: a novel multi-view graph convolutional network for identifying spatial domains with attention mechanism
0 -- 0Wenlan Chen, Hong Wang, Cheng Liang. Deep multi-view contrastive learning for cancer subtype identification
0 -- 0Weixu Wang, Xiaolan Zhou, Jing Wang, Jun Yao, Haimei Wen, Yi Wang, Mingwan Sun, Chao Zhang, Wei Tao, Jiahua Zou, Ting Ni. Approximate estimation of cell-type resolution transcriptome in bulk tissue through matrix completion
0 -- 0Guiying Wu, Mengmeng Song, Ke Wang, Tianyu Cui, Zicong Jiao, Liyan Ji, Xuan Gao, Jiayin Wang, Tao Liu, Xuefeng Xia, Huan Fang, Yanfang Guan, Xin Yi. DELFMUT: duplex sequencing-oriented depth estimation model for stable detection of low-frequency mutations
0 -- 0Yang Yue, Shu Li, Lingling Wang, Huanxiang Liu, Henry H. Y. Tong, Shan He. MpbPPI: a multi-task pre-training-based equivariant approach for the prediction of the effect of amino acid mutations on protein-protein interactions
0 -- 0Zixiao Wang, Shiyang Liang, Siwei Liu 0001, Zhaohan Meng, Jingjie Wang, Shangsong Liang. Sequence pre-training-based graph neural network for predicting lncRNA-miRNA associations
0 -- 0Yuhang Liu, Zixuan Wang, Hao Yuan, Guiquan Zhu, Yongqing Zhang. HEAP: a task adaptive-based explainable deep learning framework for enhancer activity prediction
0 -- 0Rui Fan, Xiangwen Ji, Jianwei Li, Qinghua Cui, Chunmei Cui. Defining the single base importance of human mRNAs and lncRNAs
0 -- 0Hai Yang 0002, Yawen Liu, Yijing Yang, Dongdong Li, Zhe Wang 0002. InDEP: an interpretable machine learning approach to predict cancer driver genes from multi-omics data
0 -- 0Andrea Raffo, Jonas Paulsen. The shape of chromatin: insights from computational recognition of geometric patterns in Hi-C data
0 -- 0Ailin Xie, Ziqiao Zhang, Jihong Guan, Shuigeng Zhou. Self-supervised learning with chemistry-aware fragmentation for effective molecular property prediction
0 -- 0Lin Li, Rui Xia, Wei Chen, Qi Zhao, Peng Tao, Luonan Chen. Single-cell causal network inferred by cross-mapping entropy
0 -- 0Xujun Zhang, Chao Shen, Tianyue Wang, Yafeng Deng, Yu Kang 0002, Dan Li 0013, Tingjun Hou, Peichen Pan. ML-PLIC: a web platform for characterizing protein-ligand interactions and developing machine learning-based scoring functions
0 -- 0Xuejing Shi, Juntong Zhu, Yahui Long, Cheng Liang. Identifying spatial domains of spatially resolved transcriptomics via multi-view graph convolutional networks
0 -- 0Shijie Xie, Xiaojun Xie, Xin Zhao, Fei Liu, Yiming Wang, Jihui Ping, Zhiwei Ji. HNSPPI: a hybrid computational model combing network and sequence information for predicting protein-protein interaction
0 -- 0Jinyang Wu, Zhiwei Ning, Yidong Ding, Ying Wang, Qinke Peng, Laiyi Fu. KGETCDA: an efficient representation learning framework based on knowledge graph encoder from transformer for predicting circRNA-disease associations
0 -- 0Nguyen-Quoc-Khanh Le, Wanru Li, Yanshuang Cao. Sequence-based prediction model of protein crystallization propensity using machine learning and two-level feature selection
0 -- 0Jeonghyeon Gu, Dongmin Bang, Jungseob Yi, Sangseon Lee, Dong-Kyu Kim, Sun Kim. A model-agnostic framework to enhance knowledge graph-based drug combination prediction with drug-drug interaction data and supervised contrastive learning
0 -- 0Md. Rezaul Karim 0001, Tanhim Islam, Md Shajalal, Oya Beyan, Christoph Lange 0002, Michael Cochez, Dietrich Rebholz-Schuhmann, Stefan Decker. Explainable AI for Bioinformatics: Methods, Tools and Applications
0 -- 0Dohun Yi, Jin-Wu Nam, Hyobin Jeong. Toward the functional interpretation of somatic structural variations: bulk- and single-cell approaches
0 -- 0Yao-zhong Zhang, Yunjie Liu, Zeheng Bai, Kosuke Fujimoto, Satoshi Uematsu, Seiya Imoto. Zero-shot-capable identification of phage-host relationships with whole-genome sequence representation by contrastive learning
0 -- 0Emily L. Leventhal, Andrea R. Daamen, Peter E. Lipsky. Letter to the editor: testing the effectiveness of MyPROSLE in classifying patients with lupus nephritis
0 -- 0Marc Horlacher, Giulia Cantini, Julian Hesse, Patrick Schinke, Nicolas Goedert, Shubhankar Londhe, Lambert Moyon, Annalisa Marsico. A systematic benchmark of machine learning methods for protein-RNA interaction prediction
0 -- 0Huiguang Yi, Yanling Lin, Qing Chang, Wenfei Jin. A fast and globally optimal solution for RNA-seq quantification
0 -- 0Shen Han, Haitao Fu, Yuyang Wu, Ganglan Zhao, Zhenyu Song, Feng Huang, Zhongfei Zhang, Shichao Liu, Wen Zhang 0008. HimGNN: a novel hierarchical molecular graph representation learning framework for property prediction
0 -- 0Pingjing Li, Hong Liu, Jialiang Sun, Jianguo Lu, Jian Liu. HiBrowser: an interactive and dynamic browser for synchronous Hi-C data visualization
0 -- 0Yanping Zeng, Yongxin He, Ruiqing Zheng, Min Li 0007. Inferring single-cell gene regulatory network by non-redundant mutual information
0 -- 0Tasbiraha Athaya, Rony Chowdhury Ripan, Xiaoman Li, Haiyan Hu. Multimodal deep learning approaches for single-cell multi-omics data integration